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Yorodumi- PDB-3dj9: Crystal Structure of an isolated, unglycosylated antibody CH2 domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dj9 | ||||||
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Title | Crystal Structure of an isolated, unglycosylated antibody CH2 domain | ||||||
Components | Ig gamma-1 chain C region | ||||||
Keywords | IMMUNE SYSTEM / antibody / immunoglobulin / CH2 domain / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Secreted | ||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Prabakaran, P. / Vu, B.K. / Gan, J. / Dimitrov, D.S. / Ji, X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of an isolated unglycosylated antibody C(H)2 domain. Authors: Prabakaran, P. / Vu, B.K. / Gan, J. / Feng, Y. / Dimitrov, D.S. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dj9.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dj9.ent.gz | 24.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3dj9 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3dj9 | HTTPS FTP |
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-Related structure data
Related structure data | 1hzhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12087.820 Da / Num. of mol.: 1 / Fragment: CH2 constant domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P01857 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 30% PEG 1500, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Aug 23, 2006 / Details: Mirror |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 11044 / Num. obs: 11044 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 5.4 / Num. unique all: 11044 / % possible all: 57.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HZH Resolution: 1.75→26.361 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / σ(F): 0.17 / Phase error: 23.46 / Stereochemistry target values: ML Details: THE REFINEMENT WAS DONE MAINLY WITH CNS 1.1 AND FINISHED WITH PHENIX
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.717 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.39 Å2 / Biso mean: 22.847 Å2 / Biso min: 10.37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→26.361 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Xplor file |
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